How many years had Dr. Manette been in prison when he decides to write the letter about why he was falsely imprisoned?

Dr. Manette was in prison for eighteen years, total.

If you are talking about the letter he wrote about the brother and his sister, he wrote that BEFORE he gets put in prison. If you are talking about the documentation he writes about his time in the prison that he secrets in the wall, the exact time is never specified.